Table S8:High-level Amplifications Associated with SqCC Tumors with and without BRF2 Activation1

Cytoband / q value / Wide peak boundaries2 / Candidate target
SqCC Tumors with BRF2 Copy Number Increase
3q26.2 / 0.03 / 168.23-194.13 / SOX2
8p12 / 2.90E-06 / 35.46-40.07 / BRF2
11p13 / 0.12 / 31.01-37.54 / CD44
12q14.1 / 0.16 / 59.41-64.42 / CDK43
12q15 / 0.17 / 62.99-67.60 / MDM2
SqCC Tumors without BRF2 Copy Number Increase
1p34.2 / 0.06 / 38.93-40.79 / MYCL1
3q26.33 / 2.84E-09 / 182.10-184.73 / SOX2
5p14.1 / 0.16 / 8.22-43.13 / TERT3
7p11.2 / 0.0003 / 54.16-56.13 / EGFR
8q24.21 / 0.12 / 120.28-132.17 / MYC
9p13.3 / 0.08 / 32.56-36.18 / N/A
14q32.2 / 0.20 / 96.53-100.63 / N/A
20p12.1 / 0.20 / 10.36-20.34 / N/A

192 SqCC tumors were separated based on their BRF2 copy number status (38 with BRF2 copy number increase and 54 without) and aCGH-Smooth was used to smooth ratio values and identify copy number breakpoints for each sample as described in the Methods section. The resulting segments and ratio values were then analyzed using the Genomic Identification of Significant Targets in Cancer (GISTIC) method [Beroukhim et al.Proc Natl Acad Sci U S A104:20007-12, 2007] to determine regions of significant amplification in each group. Analysis was performed using Gene Pattern software ( with default settings with the exception of the amplification threshold = 0.6. In addition, known regions of copy number variation in the normal population [Wong et al. Am J Hum Genet 80:91-104, 2007] were removed during the analysis. Lastly, only focal regions of amplification (wide peak region < chromosome arm in size) are reported.

Tumors without BRF2 increase harboured amplifications in other well-known lung cancer oncogenes including EGFR and MYC. In contrast, SqCCs with BRF2 amplification also displayed amplification of MDM2, further highlighting the potential importance of p53 inactivation in BRF2-mediated tumorigenesis. Of interest, both SqCC subsets contain amplification of chromosome arm 3q, which has previously been shown to be a frequent event in SqCC tumorigenesis. Recently, SOX2 has been identified as the target of this amplification and lineage-survival oncogene in lung and esophageal SqCCs [Bass et al. Nat Genet 41:1238-42, 2009]. Together, this preliminary investigation suggests that SqCC lung tumors with amplification of BRF2 may represent a distinct subset of SqCC that develop through a unique genetic pathway, independent of common lung cancer oncogenes such as EGFR and MYC.

2Boundaries are reported as the Mbp position on the respective chromosome.

3Gene immediately adjacent to wide-peak region.